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Sample GSM1048159 Query DataSets for GSM1048159
Status Public on Mar 06, 2013
Title Buccal cell Birth twin 2, B1042
Sample type genomic
Source name Buccal cheek swab, DZ, birth
Organism Homo sapiens
Characteristics gender: male
age: birth
cell type: normal buccal cells
monozygotic: 0
dizygotic: 1
monochorionic: 0
sibship: 6
twin: 2
Extracted molecule genomic DNA
Extraction protocol gDNA was purified from buccal swabs using phenol chloroform extraction.
Label Cy5 and Cy3
Label protocol Bisulphite conversion was carried out using the Methyl Xceed bisulphite kit as per the manufacturer's instructions.
Hybridization protocol Bisulphite-converted DNA was amplified, fragmented and hybridised to the Illumina Infinium Human Methylation27 BeadChip using the standard llumina protocol.
Scan protocol Arrays were imaged using the BeadArray Reader using the standard recommended Illumina scanner setting.
Description B1042.2_B
Data processing Data were preprocessed using the Bioconductor Minfi package in R by the 'illumina' method and normalized to control probes. Subset quantile normalization was performed on type 1 and type 2 probes. Probes failing P detection cutoff of <0.01 were removed. Probes on the X and Y chromosomes have been removed from the processed data. Outlier samples were removed. Between-array quantile normalization was performed to arrive at the final data set of 330168 probes and 53 samples.
Submission date Dec 03, 2012
Last update date Mar 06, 2013
Contact name David Martino
Phone 0863191635
Organization name Telethon Kids Institute
Street address Perth Childrens Hospital, 15 Hospital Avenue
State/province Western Australia
ZIP/Postal code 6009
Country Australia
Platform ID GPL13534
Series (1)
GSE42700 Epigenome analysis of buccal cells from monozygotic and dizygotic twins

Data table header descriptions
VALUE Quantile-normalized average Beta

Data table
cg00000957 0.82246932634523
cg00001349 0.753398957629669
cg00001583 0.0291185193950418
cg00002028 0.0631876467312114
cg00003202 0.0168577736308283
cg00003287 0.0742118314038024
cg00004121 0.4743786796582
cg00007036 0.941974176121549
cg00007898 0.0263843945870434
cg00008004 0.134756860610663
cg00008647 0.0676772753922328
cg00009292 0.185009428368343
cg00009916 0.0142094262822553
cg00011717 0.918166504838974
cg00014168 0.849320248236679
cg00015286 0.801995954074156
cg00015930 0.958488874722039
cg00016238 0.828720971416682
cg00017221 0.0313766827088994
cg00017437 0.0237120353637418

Total number of rows: 330168

Table truncated, full table size 9433 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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